--------------------------------------------------------------------------------
|             Helix Systems -- Center for Information Technology               |
|                            http://helix.nih.gov                              |
|   National Institutes of Health, Department of Health and Human Services     |
|                                                                              |
|             DNAWorks Web Site: http://helixweb.nih.gov/dnaworks              |
--------------------------------------------------------------------------------
|                                                                              |
|              Send all correspondence to webtools@helix.nih.gov               |
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 Job started on 09/02/2013 at 15:05:10

 Job name: CC_090213_S_agalactiae_STP1                                          

 Output will be sent to caroline.chen1101@gmail.com   
 
      SEQUENCE  1: PROTEIN LENGTH =  246                               
 ----------------------------------------------------------------
   1 MEISLLTDIGQRRSNNQDFINQFENKAGVPLIILADGMGGHRAGNIASEMTVTDLGSDWA
  61 ETDFSELSEIRDWMLVSIETENRKIYELGQSDDYKGMGTTIEAVAIVGDNIIFAHVGDSR
 121 IGIVRQGEYHLLTSDHSLVNELVKAGQLTEEEAASHPQKNIITQSIGQANPVEPDLGVHL
 181 LEEGDYLVVNSDGLTNMLSNADIATVLTQEKTLDDKNQDLITLANHRGGLDNITVALVYV
 241 ESEAVX
 ----------------------------------------------------------------
 
             CODON FREQUENCY TABLE: E. coli Class II              
 ----------------------------------------------------------------
 
      TTT F 0.291   TCT S 0.324   TAT Y 0.352   TGT C 0.389
      TTC F 0.709   TCC S 0.266   TAC Y 0.648   TGC C 0.612
      TTA L 0.034   TCA S 0.048   TAA X 0.630   TGA X 0.352
      TTG L 0.055   TCG S 0.074   TAG X 0.076   TGG W 1.000
 
      CTT L 0.056   CCT P 0.112   CAT H 0.298   CGT R 0.643
      CTC L 0.080   CCC P 0.016   CAC H 0.702   CGC R 0.330
      CTA L 0.008   CCA P 0.153   CAA Q 0.187   CGA R 0.011
      CTG L 0.767   CCG P 0.719   CAG Q 0.814   CGG R 0.008
 
      ATT I 0.335   ACT T 0.291   AAT N 0.173   AGT S 0.045
      ATC I 0.659   ACC T 0.536   AAC N 0.828   AGC S 0.243
      ATA I 0.006   ACA T 0.047   AAA K 0.786   AGA R 0.006
      ATG M 1.000   ACG T 0.127   AAG K 0.215   AGG R 0.003
 
      GTT V 0.398   GCT A 0.275   GAT D 0.461   GGT G 0.508
      GTC V 0.135   GCC A 0.161   GAC D 0.540   GGC G 0.428
      GTA V 0.200   GCA A 0.240   GAA E 0.754   GGA G 0.020
      GTG V 0.268   GCG A 0.323   GAG E 0.247   GGG G 0.044
 
 
             ACTIVE CODONS FOR SEQUENCE GENERATION 
 
  Residue   Codons   Active Codons     Min. Freq.    Max. Freq.
 ----------------------------------------------------------------
   A  Ala      4           4             0.161         0.323
   C  Cys      2           2             0.389         0.612
   D  Asp      2           2             0.461         0.540
 
   E  Glu      2           2             0.247         0.754
   F  Phe      2           2             0.291         0.709
   G  Gly      4           2             0.428         0.508
 
   H  His      2           2             0.298         0.702
   I  Ile      3           2             0.335         0.659
   K  Lys      2           2             0.215         0.786
 
   L  Leu      6           2             0.080         0.767
   M  Met      1           1             1.000         1.000
   N  Asn      2           2             0.173         0.828
 
   P  Pro      4           3             0.112         0.719
   Q  Gln      2           2             0.187         0.814
   R  Arg      6           2             0.330         0.643
 
   S  Ser      6           3             0.243         0.324
   T  Thr      4           3             0.127         0.536
   V  Val      4           4             0.135         0.398
 
   W  Trp      1           1             1.000         1.000
   X  End      3           2             0.352         0.630
   Y  Tyr      2           2             0.352         0.648
 
 
                SEQUENCE PATTERNS TO BE SCREENED
 ----------------------------------------------------------------
 ----------------------------------------------------------------
 
 ----------------------------------------------------------------
                    PARAMETERS FOR TRIAL 1                             
 ----------------------------------------------------------------
               Total Size Of Gene ......... 738 nt                        
               Protein Residues ........... 246                           
               Mutatable Residues ......... 238                           
               Fixed Nucleotides .......... 24 nt                         
               Degenerate Nucleotides ..... 0 nt                          
               Oligo Size ................. 60 nt                         
               Annealing Temp ............. 62 +/- 1*C                    
               Oligo Concentration ........ 1.00E-7 M                     
               Sodium Concentration ....... 5.00E-2 M                     
               Mg2+ Concentration ......... 2.00E-3 M                     
               Codon Frequency Threshold .. 10%                           
               Repeat Threshold ........... 8 nt                          
               Mispriming Threshold ....... 8/18 (6 exact) nt             
 
--------------------------------------------------------------------------------
 
 The DNA sequence #   1 is:
 ----------------------------------------------------------------
   1 ATGGAAATCTCTCTCCTGACTGACATCGGTCAACGTCGCTCTAATAACCAGGACTTCATC
  61 AATCAGTTCGAAAACAAGGCCGGTGTTCCGCTCATCATCCTGGCGGACGGCATGGGCGGT
 121 CACCGTGCGGGTAACATTGCGAGCGAAATGACCGTTACCGATCTGGGCTCTGACTGGGCG
 181 GAAACCGACTTCTCTGAACTGTCTGAAATCCGTGACTGGATGCTCGTTTCTATCGAAACG
 241 GAAAACCGTAAAATCTACGAACTGGGTCAGTCTGACGACTACAAAGGTATGGGTACCACC
 301 ATCGAAGCGGTTGCGATCGTTGGCGACAACATCATCTTCGCGCACGTTGGTGACTCTCGT
 361 ATCGGTATCGTTCGTCAGGGTGAATACCATCTGCTGACTTCCGACCACTCTCTGGTTAAC
 421 GAGCTGGTGAAAGCGGGTCAACTGACCGAAGAAGAAGCGGCGTCTCACCCGCAGAAGAAT
 481 ATCATCACCCAGTCTATTGGCCAGGCGAACCCGGTTGAACCGGACCTGGGCGTCCACCTG
 541 CTGGAAGAAGGTGACTACCTGGTTGTTAACTCTGACGGTCTGACCAACATGCTGTCTAAC
 601 GCGGACATCGCGACCGTTCTGACGCAGGAAAAAACCCTGGACGACAAAAATCAGGACCTG
 661 ATCACTCTCGCTAACCATCGTGGTGGTCTGGACAATATTACCGTTGCGCTGGTATACGTT
 721 GAATCTGAAGCTGTTTAA
 ----------------------------------------------------------------
 
 The oligonucleotide assembly is:
 ----------------------------------------------------------------
     1       10        20        30        40        50        60
     |        |         |         |         |         |         |
 
     1 --->                                                      
   1 ATGGAAATCTCTCTCCTGACTGACATCGGTCAACGTCGCTCTAATAACCAGGACTTCA  
                                         GCGAGATTATTGGTCCTGAAGTAG
                                                                 
      M  E  I  S  L  L  T  D  I  G  Q  R  R  S  N  N  Q  D  F  I 
 
     |        |         |         |         |         |         |
 
                        3 --->                                   
  61                    ccggtgttccgctcatcatcctggcggacggcatgggcggt
     TTAGTCAAGCTTTTGTTCCGGCCACAAGGCGAGTAG                        
                                  <---  2                        
      N  Q  F  E  N  K  A  G  V  P  L  I  I  L  A  D  G  M  G  G 
 
     |        |         |         |         |         |         |
 
                                                  5 --->         
 121 caccgtgcgggtaacattg                          GGCTCTGACTGGGCG
      tggcacgcccattgtaacgctcgctttactggcaatggctagacccgagactgacccgc
                                                           <---  
      H  R  A  G  N  I  A  S  E  M  T  V  T  D  L  G  S  D  W  A 
 
     |        |         |         |         |         |         |
 
                                                                 
 181 GAAACCGACTTCTCTGAACTGTCTGAAATCCGTGACTGGATGCTC               
     c                        TTTAGGCACTGACCTACGAGCAAAGATAGCTTTGC
     4                                                           
      E  T  D  F  S  E  L  S  E  I  R  D  W  M  L  V  S  I  E  T 
 
     |        |         |         |         |         |         |
 
       7 --->                                                    
 241   aaaccgtaaaatctacgaactgggtcagtctgacgactacaaaggtatgggtaccacc
     CTTTTGGCATTTTAGATGCTTGACC                gtttccatacccatggtgg
                       <---  6                                   
      E  N  R  K  I  Y  E  L  G  Q  S  D  D  Y  K  G  M  G  T  T 
 
     |        |         |         |         |         |         |
 
                           9 --->                                
 301 at                    GCGACAACATCATCTTCGCGCACGTTGGTGACTCTCGT
     tagcttcgccaacgctagcaaccgctgttgtagtagaagcg                   
                                       <---  8                   
      I  E  A  V  A  I  V  G  D  N  I  I  F  A  H  V  G  D  S  R 
 
     |        |         |         |         |         |         |
 
                                               11 --->           
 361 ATCGGTATCGTTCGTCAGGGTG                    gaccactctctggttaac
        CCATAGCAAGCAGTCCCACTTATGGTAGACGACTGAAGGCTGGTGAGAGACCAATTG
                                                             <---
      I  G  I  V  R  Q  G  E  Y  H  L  L  T  S  D  H  S  L  V  N 
 
     |        |         |         |         |         |         |
 
                                                                 
 421 gagctggtgaaagcgggtcaactgaccgaagaagaagcggcg                  
     CTC                      ggcttcttcttcgccgcagagtgggcgtcttctta
      10                                                         
      E  L  V  K  A  G  Q  L  T  E  E  E  A  A  S  H  P  Q  K  N 
 
     |        |         |         |         |         |         |
 
           13 --->                                               
 481       ACCCAGTCTATTGGCCAGGCGAACCCGGTTGAACCGGACCTGGGCGTCCACCTG
     tagtagtgggtcagataaccggtcc                        CGCAGGTGGAC
                       <--- 12                                   
      I  I  T  Q  S  I  G  Q  A  N  P  V  E  P  D  L  G  V  H  L 
 
     |        |         |         |         |         |         |
 
                                   15 --->                       
 541 CTGGAA                        tctgacggtctgaccaacatgctgtctaac
     GACCTTCTTCCACTGATGGACCAACAATTGAGACTGCCAGACTGGTTGT           
                                               <--- 14           
      L  E  E  G  D  Y  L  V  V  N  S  D  G  L  T  N  M  L  S  N 
 
     |        |         |         |         |         |         |
 
                                                          17 --->
 601 gcggacatcgcgaccgttctgacgcaggaa                       GGACCTG
                 tggcaagactgcgtccttttttgggacctgctgtttttagtcctggac
                                                                 
      A  D  I  A  T  V  L  T  Q  E  K  T  L  D  D  K  N  Q  D  L 
 
     |        |         |         |         |         |         |
 
                                                                 
 661 ATCACTCTCGCTAACCATCGTGGTGGTCTGGACAATATTACCGTTGCGCTGGT       
     tagtgagagcga                     TTATAATGGCAACGCGACCATATGCAA
          <--- 16                                                
      I  T  L  A  N  H  R  G  G  L  D  N  I  T  V  A  L  V  Y  V 
 
     |        |         |         |         |         |         |
 
                       
 721                   
     CTTAGACTTCGACAAATT
                <--- 18
      E  S  E  A  V  X 
 ----------------------------------------------------------------
 
 The total codon usage score ...........     0.000
 The total length score ................     0.000
 The total melting temperature score ...     0.000
 The total repeat score ................     0.000
 The total pattern score ...............     0.000
 The total mispriming score ............     0.000
 The total AT content score ............     0.000
 The total GC content score ............     0.000
 The total fixed gap score .............      N/A
                The OVERALL score ......     0.000
 
 
                  DETAILED CODON FREQUENCY REPORT 
  [ Codon, AA, Frequency, # of times used in coding sequence ] 
 ----------------------------------------------------------------
 
 TTT F 0.29   0  TCT S 0.32  14  TAT Y 0.35   0  TGT C 0.39   0
 TTC F 0.71   4  TCC S 0.27   1  TAC Y 0.65   5  TGC C 0.61   0
 TTA L 0.03   0  TCA S 0.05   0  TAA X 0.63   1  TGA X 0.35   0
 TTG L 0.06   0  TCG S 0.07   0  TAG X 0.08   0  TGG W 1.00   2
 
 CTT L 0.06   0  CCT P 0.11   0  CAT H 0.30   2  CGT R 0.64   7
 CTC L 0.08   4  CCC P 0.02   0  CAC H 0.70   5  CGC R 0.33   1
 CTA L 0.01   0  CCA P 0.15   0  CAA Q 0.19   2  CGA R 0.01   0
 CTG L 0.77  21  CCG P 0.72   4  CAG Q 0.81   9  CGG R 0.01   0
 
 ATT I 0.34   3  ACT T 0.29   3  AAT N 0.17   5  AGT S 0.05   0
 ATC I 0.66  18  ACC T 0.54  11  AAC N 0.83  11  AGC S 0.24   1
 ATA I 0.01   0  ACA T 0.05   0  AAA K 0.79   5  AGA R 0.01   0
 ATG M 1.00   6  ACG T 0.13   2  AAG K 0.22   2  AGG R 0.00   0
 
 GTT V 0.40  15  GCT A 0.28   2  GAT D 0.46   1  GGT G 0.51  15
 GTC V 0.14   1  GCC A 0.16   1  GAC D 0.54  19  GGC G 0.43   6
 GTA V 0.20   1  GCA A 0.24   0  GAA E 0.75  20  GGA G 0.02   0
 GTG V 0.27   1  GCG A 0.32  14  GAG E 0.25   1  GGG G 0.04   0
 
             
              Frequency Range   Number of Codons
             -------------------------------------
                0% -  4%                  0
                5% -  9%                  4
               10% - 14%                  3
               15% - 19%                  8
               20% - 24%                  5
               25% - 29%                  9
               30% - 34%                 32
               35% - 39%                 15
               40% - 44%                  6
               45% - 49%                  1
                  >= 50%                163
             -------------------------------------
              Total Codons Used =   246
 
                  Tm Range    # of Overlaps 
             -------------------------------------
                   <60            0
                    60            0
                    61            7
                    62           10
                    63            0
                    64            0
                    65            0
                    66            0
                    67            0
                  >=68            0
             -------------------------------------
              Tm Range =  1.9
 
              Ovrlap Len Range  # of Oligos
             -------------------------------------
                   <16            0
                    16            1
                    17            3
                    18            2
                    19            5
                    20            2
                    21            2
                    22            1
                    23            1
                    24            0
                    25            0
                  >=26            0
             -------------------------------------
              Lowest Overlap = 16
 
              Length Range   # of Oligos
             -------------------------------------
                   < 51            1
                   51- 52           0
                   53- 54           0
                   55- 56           0
                   57- 58           1
                   59- 60          16
                   61- 62           0
                   63- 64           0
                   65- 66           0
                   67- 68           0
                   69- 70           0
                   >= 71           0
             -------------------------------------
              Longest =  60
 
 
          Sequence Patterns Screened (As Supplied By User)
 ----------------------------------------------------------------
                       None found
 ----------------------------------------------------------------
 
        18 oligonucleotides need to be synthesized
 ----------------------------------------------------------------
  1 ATGGAAATCTCTCTCCTGACTGACATCGGTCAACGTCGCTCTAATAACCAGGACTTCA  58
  2 GATGAGCGGAACACCGGCCTTGTTTTCGAACTGATTGATGAAGTCCTGGTTATTAGAGCG  60
  3 CCGGTGTTCCGCTCATCATCCTGGCGGACGGCATGGGCGGTCACCGTGCGGGTAACATTG  60
  4 CCGCCCAGTCAGAGCCCAGATCGGTAACGGTCATTTCGCTCGCAATGTTACCCGCACGGT  60
  5 GGCTCTGACTGGGCGGAAACCGACTTCTCTGAACTGTCTGAAATCCGTGACTGGATGCTC  60
  6 CCAGTTCGTAGATTTTACGGTTTTCCGTTTCGATAGAAACGAGCATCCAGTCACGGATTT  60
  7 AAACCGTAAAATCTACGAACTGGGTCAGTCTGACGACTACAAAGGTATGGGTACCACCAT  60
  8 GCGAAGATGATGTTGTCGCCAACGATCGCAACCGCTTCGATGGTGGTACCCATACCTTTG  60
  9 GCGACAACATCATCTTCGCGCACGTTGGTGACTCTCGTATCGGTATCGTTCGTCAGGGTG  60
 10 CTCGTTAACCAGAGAGTGGTCGGAAGTCAGCAGATGGTATTCACCCTGACGAACGATACC  60
 11 GACCACTCTCTGGTTAACGAGCTGGTGAAAGCGGGTCAACTGACCGAAGAAGAAGCGGCG  60
 12 CCTGGCCAATAGACTGGGTGATGATATTCTTCTGCGGGTGAGACGCCGCTTCTTCTTCGG  60
 13 ACCCAGTCTATTGGCCAGGCGAACCCGGTTGAACCGGACCTGGGCGTCCACCTGCTGGAA  60
 14 TGTTGGTCAGACCGTCAGAGTTAACAACCAGGTAGTCACCTTCTTCCAGCAGGTGGACGC  60
 15 TCTGACGGTCTGACCAACATGCTGTCTAACGCGGACATCGCGACCGTTCTGACGCAGGAA  60
 16 AGCGAGAGTGATCAGGTCCTGATTTTTGTCGTCCAGGGTTTTTTCCTGCGTCAGAACGGT  60
 17 GGACCTGATCACTCTCGCTAACCATCGTGGTGGTCTGGACAATATTACCGTTGCGCTGGT  60
 18 TTAAACAGCTTCAGATTCAACGTATACCAGCGCAACGGTAATATT  45
 
                          FINAL SUMMARY FOR   1 SOLUTION   
--------------------------------------------------------------------------------
  #    Tm   Len  |    Score   TmRange  Short    Long   #Olig  #Repeat #Misprime
 
  1    62    60  |    0.000       1.9      16      60      18       0       0
 
--------------------------------------------------------------------------------
|             Helix Systems -- Center for Information Technology               |
|                            http://helix.nih.gov                              |
|   National Institutes of Health, Department of Health and Human Services     |
|                                                                              |
|             DNAWorks Web Site: http://helixweb.nih.gov/dnaworks              |
--------------------------------------------------------------------------------
